Are you using the iOS 5 updated clock hide? Or are you using the one from iOS 4? I know they just recently released the clock hide for iOS 5 and it has an interface within the settings.app to turn it off or on. If its the one for ios 5 go into settings and see if it's applied. If that's not the issue then uninstall and reinstall clock hide for iOS 5, make sure it's enabled and working THEN apply the LS theme you want.

I'm sorry I didn't notice that's it's the transparent bar behind the clock. The issue that still remains with some themes is that the BarLCD file is in whatever theme you applied (if u have an UI theme/complete. I was having that same issue and then I changed my theme to dark hollow and that transparent clock bar disappeared with iOS 5 clockhide

Ok wait, did you actually download this clockhide from cydia or did you edit the .plist file to do this? Before the actual packages were released on cydia I also tried editing the .plist instructions and I had the exact same issue. If you edited the .plist and replaced the BarLCD files and stuff put those back to the way they were originally (hopefully you backed them up). Then go to Cydia and install an actual package for it. If you in fact already have a cydia package installed then delete it and find "Clockhide-PK" and install that. If you cannot find it PM me and I'll give you the source for it (I do not list ANY sources here because I've gotten violations for doing so, even though it's for a non piracy source addon).

Ok I see you do have it from cydia so follow the bottom instructions. Sorry I had surgery this morning and am having a hard time remembering what I read lol. GOOD DRUGS lol

I wouldn't do that. I have it from Cydia and it works great. Thats the thing I did and it caused my phone to not respring and stuff. I hope you have better luck than I did with it but if not get that package I talked about. That plist tweak really screwed up my phone. Just know you have to reapply those changes EVERYTIME you Change your theme.